This glyph draws DNA sequences. At high magnifications, this glyph will draw the actual base pairs of the sequence (both strands). At low magnifications, the glyph will plot the GC content. By default, the GC calculation will use non-overlapping bins, but this can be changed by specifying the gc_window option, in which case, a sliding window calculation will be used.

For this glyph to work, the feature must return a Bio::PrimarySeq DNA object in response to the seq() method. For example, you can use a Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq like this:

In addition to the common options, the following glyph-specific options are recognized:

Option Description Default
------ ----------- -------
-do_gc Whether to draw the GC true
graph at low mags
-gc_window Size of the sliding window E<lt>noneE<gt>
to use in the GC content
calculation. If this is
not defined, non-
overlapping bins will be
used. If this is set to
"auto", then the glyph will
choose a window equal to
1% of the interval.
-gc_bins Fixed number of intervals 100
to sample across the
panel.
-axis_color Color of the vertical axes fgcolor
in the GC content graph
-strand Show both forward and auto
reverse strand, one of
"forward", "reverse",
"both" or "auto".
In "auto" mode,
+1 strand features will
show the plus strand
-1 strand features will
show the reverse complement
and strandless features will
show both

NOTE: -gc_window=>'auto' gives nice results and is recommended for drawing GC content. The GC content axes draw slightly outside the panel, so you may wish to add some extra padding on the right and left.